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Filters

Filters have been set

Use the range slider to set the general start and end coordinates for
the view, or switch to the "from" and "to" entry fields in order to
give precise coordinates.

Coordinate system

Amino-acid

cDNA

Tissue

Screen type

Whole genome screen

Targeted screen

All

Somatic status

Confirmed somatic

Previously reported

Variant of unknown origin

Sample type

Cultured

Tumour sample

Mutation impact

The mutation impact filters are derived from the FATHMM-MKL algorithm
(Functional Analysis through Hidden Markov Models).
FATHMM-MKL is an algorithm which predicts the functional, molecular
and phenotypic consequences of protein missense variants using hidden
Markov models.

Where FATHMM-MKL scores are ≥ 0.7 the mutation is classified
as 'pathogenic', or 'neutral' if the score is ≤ 0.5. You can find
more information about FATHMM scores on the
FATHMM website.

Pathogenic

Neutral

Mutation Type

Complex

Deletion

Frameshift

Inframe

Insertion

Frameshift

Inframe

Substitution

Missense

Nonsense

Synonymous

Copy Number Variation

Include non-numeric data

Gain

Loss

Some copy number data is descriptive with no associated numeric
data for minor allele or total copy number. These data are not
informative for defining high level amplification, homozygous
deletion or LOH and are excluded by default. To include these
data, check this box.

GRCh38
·
COSMIC v89

The gene view histogram is a graphical view of mutations across KIR3DL2.
These mutations are displayed at the amino acid level across the
full length of the gene by default. Restrict the view to a region of
the gene by dragging across the histogram to highlight the region of
interest, or by using the sliders in the filters panel to the left.
Show more

This default peptide view shows a histogram of single base
substitutions, colour coded by residue according to the colour scheme
used in Ensembl. Under this is shown the amino acid sequence and the
Pfam protein structures, followed by complex mutations and insertions
and deletions. The graphical view can be switched to cDNA coordinates
by selecting from the "Coordinate system" options in the "Filters"
panel on the left.

You can use the filters panel to select the types of data that are
displayed. After adjusting a filter, press Apply
filters, or press Reset filters to revert to the
original, unfiltered display.

This section shows the drugs associated with
KIR3DL2 resistance mutations. In the tabs
below you can see any other genes that have resistance mutations to the
same drug(s), and the distribution of mutations that occur in those
genes.

The table shows the distribution of mutations across the primary tissue
types that are curated by COSMIC. Histograms show the percentage of
mutated samples for point mutations, CNV data and gene expression data.
Moving your mouse over the histograms will show additional data.

You can see additional information about the data presented here in the
help pages.

The genome browser shows COSMIC annotations for KIR3DL2 in a genomic context.
Show more

Note: in some web browsers the genome browser
may display a blank content panel when switching between browser
tabs or when returning to the page using the browser's Back
button. If this happens please click and drag the blank content panel to
reload the genome browser.

This section displays a series of charts that show the distribution of
different types of mutations for KIR3DL2.
Show more

The first chart in this section shows a summary of the types of
mutation that have been observed in samples for this gene. The table
shows the number of samples recorded as having a particular type of
mutation, with the number in brackets giving the percentage of
samples with that type of mutation.

Note that a sample may have more than one type of
mutation, so the total number of samples determined by simply summing the
values in the table may not match the total number of unique samples
given under the table. For the same reason, summing the percentages in
the table may give a value of greater than 100%.

This tab displays a table of mutations for the selected gene. You can see
more information in our
help pages.

Position (AA)

Mutation (CDS)

Mutation (Amino Acid)

Mutation ID (COSM)

Count

Mutation Type

This tab displays a table of fusions for the selected gene. You can see
more information in our
help pages.

Mutation (Amino Acid)

Mutation ID (COSF)

Count

Mutation Type

This tab shows a table of gene expression and copy number variation (CNV)
data for the selected gene with links to Sample, Study, CNV and (icons) to
the ChromoView page (to view CNVs across the whole chromosome), the COSMIC
Genome Browser and Ensembl. You can see more information in our
help pages.

Table Information

Hide

The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Sample

Expression

Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type

Minor Allele

Copy Number

CN SegmentPosition

Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Study

CNV

This page contains the complete Methylation data for the gene and filter
selection(s). Each Methylation probe links to the COSMIC Genome Browser and
Ensembl. You can see more information in out
help pages.

Sample Name

Sample ID

Probe ID

Probe Posn.

Type

High (Hypermethylation); Beta-Value > 0.8 and differs from normal average by > 0.5

Low (Hypomethylated); Beta-Value < 0.2 and differs from normal average by > 0.5